After learning Sheldon went behind their backs to work with the military again, Leonard and Howard say Sheldon is like Thomas Edison, taking credit for others' ideas, while they are more like Nikola Tesla. Leonard and Howard bring in Barry Kripke to help create a better idea than Sheldon's, but Kripke goes to the military himself, cutting all three of them out. Meanwhile, Bernadette fears Ruchi is trying to steal her projects at work while she is on maternity leave and enlists Raj to spy on her. Though he finds proof that Ruchi may be stealing from Bernadette, Raj tries to defend Ruchi like a boyfriend would, pointing out Bernadette's hypocrisy as she would most likely have stolen from other people's projects as well. Ruchi is not happy about this and promptly dumps Raj.
According to Steve Holland who is the show-runner starting with this season, Wil Wheaton will return in this season since his absence from Season 10. And this has confirmed to be true since it has been stated that he reappeared in "The Proton Regeneration" (S11E6), along with Professor Proton, their first appearances since "The Opening Night Excitation" (S9E11) and "The Celebration Experimentation", respectively and a span of 43 episodes and a span of 37 episodes, respectively. Wil also returned in the 15th episode. Wil will also return for Sheldon and Amy's Wedding.
In the third-season finale, Raj and Howard sign Sheldon up for online dating to find a woman compatible with Sheldon and discover neurobiologist Amy Farrah Fowler. Like him, she has a history of social ineptitude and participates in online dating only to fulfill an agreement with her mother. This spawns a storyline in which Sheldon and Amy communicate daily while insisting to Leonard and Penny that they are not romantically involved. In "The Agreement Dissection", Sheldon and Amy talk in her apartment after a night of dancing and she kisses him on the lips. Instead of getting annoyed, Sheldon says "fascinating" and later asks Amy to be his girlfriend in "The Flaming Spittoon Acquisition". The same night he draws up "The Relationship Agreement" to verify the ground rules of him as her boyfriend and vice versa (similar to his "Roommate Agreement" with Leonard). Amy agrees but later regrets not having had a lawyer read through it.
Wednesday night is the group's designated "comic book night" because that is the day of the week when new comic books are released. The comic book store is run by fellow geek and recurring character Stuart. On a number of occasions, the group members have dressed up as pop culture characters, including The Flash, Aquaman, Frodo Baggins, Superman, Batman, Spock, The Doctor, Green Lantern, and Thor. As a consequence of losing a bet to Stuart and Wil Wheaton, the group members are forced to visit the comic book store dressed as Catwoman, Wonder Woman, Batgirl, and Supergirl. DC Comics announced that, to promote its comics, the company will sponsor Sheldon wearing Green Lantern T-shirts.
The episode opens with a short montage of clips from the series' twelve seasons, then segues to Sheldon and Amy, who are up late waiting for a call from the Nobel Committee. Following a prank call from Kripke, they are told they've won the Nobel Prize in Physics for their super-asymmetry work. The attention from the media and the university bothers Sheldon. Amy is saddened by an unflattering picture of her in a news report, so Raj convinces her to get a makeover. She loves her new look but Sheldon demands she change it back. Leonard calls him out for being rude, but Sheldon flees when he sees Penny emerge from the newly repaired elevator. Sheldon and Penny go to the Cheesecake Factory and Penny tells Sheldon that change is the only constant thing in life. On a TV, they see Bernadette and Howard take credit as Sheldon and Amy's best friends. Raj and Leonard defend Amy, with Leonard accidentally breaking Sheldon's DNA molecule model in Apartment 4A. Penny convinces Sheldon to ride in the elevator.
The show's pilot episode premiered on September 24, 2007. This was the second pilot produced for the show. A different pilot was produced for the 2006–07 television season but never aired. The structure of the original unaired pilot was substantially different from the series' current form. The only main characters retained in both pilots were Leonard (Johnny Galecki) and Sheldon (Jim Parsons), who are named after Sheldon Leonard, a longtime figure in episodic television as producer, director and actor. A minor character, Althea (Vernee Watson), appeared in the first scene of both pilots that was retained generally as-is. The first pilot included two female lead characters - Katie, "a street-hardened, tough-as-nails woman with a vulnerable interior" (played by Canadian actress Amanda Walsh) and Gilda, a scientist colleague and friend of the male characters (played by Iris Bahr). Sheldon and Leonard meet Katie after she breaks up with a boyfriend and they invite her to share their apartment. Gilda is threatened by Katie's presence. Test audiences reacted negatively to Katie, but they liked Sheldon and Leonard. The original pilot used Thomas Dolby's hit "She Blinded Me with Science" as its theme song.
Howard dresses as Sheldon for Halloween at work, hurting Sheldon's feelings. When Howard does not apologize, Amy and Sheldon dress as Bernadette and Howard at Penny and Leonard's party, angering Bernadette. Sheldon and Bernadette later bond over their painful childhood memories. Leonard is upset that Penny does not seem to remember that their first kiss was on Halloween. Penny later admits she does remember, but does not like to think of their first kiss as an unromantic drunken hookup. She likes to imagine their first kiss was one they shared on Leonard's birthday, which pleases him.
After Sheldon has a food truck moved away from the building, Leonard and Penny are shocked to find he is the leader and sole member of the Tenants' Association for the building. Amy doesn't want to be caught in the middle but secretly suggests they rally support from the other tenants to vote Sheldon out. Nobody else supports Leonard so Amy tells them Sheldon was never added to the lease when he moved across the hall with her. Sheldon fires back with his own legal technicality so Amy is forced to support Leonard. She makes Sheldon happy by saying he can be Leonard's official opposition, making Leonard believe he made a mistake. Meanwhile, Howard and Raj find a drone. Raj returns it to the cute owner Cynthia and gets her number. Unfortunately, Cynthia watches footage of Raj on the drone and is immediately turned off.
However, no legal action was required to end production of the other show: as soon as it became known that the show was unlicensed, the actors quit and the producers canceled it. Dmitriy Tankovich (who plays Leonard's counterpart, "Seva") said in an interview, "I'm upset. At first, the actors were told all legal issues were resolved. We didn't know it wasn't the case, so when the creators of The Big Bang Theory started talking about the show, I was embarrassed. I can't understand why our people first do, and then think. I consider this to be the rock bottom of my career. And I don't want to take part in a stolen show".